The classrooms at John Endecott Memorial Academy are located along the interior side of the corridors and while some of them feature the same slippery lacquered floor as the corridors others instead have a restored wooden floor, part of a restoration project that was never fully completed before the school went public. The classrooms themselves have windows that look out into the corridors where light from the corridor windows filters in. Due to the original construction of the building, not all of the classrooms are a uniform size. But they are all close enough in shape to be useful for most regular classes.

Despite the name, the computer plaza is merely just the name for the computer labs and is located on the second floor. The computers, in a surprise to all the students, are relatively state of the art. The computers in the plaza are set up on circular desks that sit in the middle of the room with wheely chairs set up around them. A desk and a projector screen are located at the front of the room for teachers to give lectures from.

The experimentation laboratory is the shared space for all science classes. As such, there is a varied selection of equipment within the room for all manner of classes. The desks in the laboratory are arranged to all face the teachers' desk at the front of the classroom. The desks however are designed in a zig-zag shape which can fit eight people, two per zig or zag. There are additional workspaces at the side of the room although these are only used when practical work is being conducted. The other most distinctive aspect of the experimentation laboratory is a large faded pink stain splattered across the ceiling as a result of a student practical gone wrong.